Question: Venn Diagramm or Alternative: Compare Protein Lists and add Annotation: Cellular Component
0
gravatar for Benni
3.8 years ago by
Benni30
Benni30 wrote:

I want to compare protein lists (Uniprot Acc) in a Venn Diagramm or an alternative (Venn only works for max. 3 Lists?). Then I want to take the unique proteins for every list and make a cake diagramm of every list, which shows the distribution of the Cellular Component Annotation. Eg. The unique proteins in list 4 are 60% membrane associated.

Do you know a good tool for that?, a Tutorial? I would prefer: Python, Cytoscape, a Website, maybe Bioconductor?

UPDATE: I think I will use matplotlib-venn for the Venn Diagram. But how can I annotate the Protein lists with the GO Terms? I don´t want to be to specific with the Term, but also not to general. I can use http://www.pantherdb.org/ to get a pie chart of my gene list with the Cellular Component Ontology. But half of the pie is then "cell part" which is to general. The childs are: intracellular (GO:0005622) and plasma membrane (GO:0005886). I want to distiguish between both components in the final pie chart. So is their a way to map GO Terms to a protein list with regard of the GO Term "depth"/"level"?

venn protein go annotation • 1.7k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Benni30

Not used it and not one of the tools you mentioned but looks promising https://cran.r-project.org/web/packages/UpSetR/

ADD REPLYlink written 3.8 years ago by microfuge1.6k

The package venneuler can take more than 3 lists.

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche22k
2
gravatar for WouterDeCoster
3.8 years ago by
Belgium
WouterDeCoster43k wrote:

Have a look at this code I wrote some time ago: Executes as python genevenn.py file1 file2 [file3]

It will save a venn diagram of 2 or 3 sets and also open the plot. It will also write the sets to a file. Standard it assumes your file has no header, but with -h you can change this. With -names you can give names to your sets, but standard the file names are used for convenience. Handling arguments could have been better but well this works.

If you know a bit of python it is pretty straightforward to edit for your convenience ;-)

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by WouterDeCoster43k
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